GeneBe

PGS1

phosphatidylglycerophosphate synthase 1

Basic information

Region (hg38): 17:78378649-78425114

Links

ENSG00000087157 ∙ NCBI:9489 ∙ OMIM:614942 ∙ HGNC:30029 ∙ Uniprot:Q32NB8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PGS1 gene.

  • not_specified (71 variants)
  • Inborn_genetic_diseases (12 variants)
  • not_provided (5 variants)
  • DNAH17-related_disorder (3 variants)
  • High_myopia (1 variants)
  • PGS1-related_disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PGS1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000024419.5. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
2
clinvar
 2
missense
69
clinvar
1
clinvar
 70
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 69 3 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
PGS1protein_codingprotein_codingENST00000262764 946475
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
1.26e-110.3161248680501249180.000200
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.502543310.7680.00002113554
Missense in Polyphen6889.5990.75894864
Synonymous-0.6701551451.070.000009341178
Loss of Function1.042025.70.7780.00000137267

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0003950.000389
Ashkenazi Jewish0.0005960.000596
East Asian0.0001110.000111
Finnish0.0001860.000186
European (Non-Finnish)0.0001620.000159
Middle Eastern0.0001110.000111
South Asian0.0002620.000261
Other0.0001650.000164

dbNSFP

Source: dbNSFP

Function
FUNCTION: Functions in the biosynthesis of the anionic phospholipids phosphatidylglycerol and cardiolipin. {ECO:0000250}.;
Pathway
Glycerophospholipid metabolism - Homo sapiens (human);Phospholipid Biosynthesis;Metabolism of lipids;cardiolipin biosynthesis;Metabolism;Glycerophospholipid biosynthesis;Phospholipid metabolism;Synthesis of PG (Consensus)

Recessive Scores

pRec
0.130

Intolerance Scores

loftool
0.361
rvis_EVS
-0.34
rvis_percentile_EVS
30.56

Haploinsufficiency Scores

pHI
0.395
hipred
Y
hipred_score
0.541
ghis
0.559

Essentials

essential_gene_CRISPR
E
essential_gene_CRISPR2
E
essential_gene_gene_trap
E
gene_indispensability_pred
N
gene_indispensability_score
0.395

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Pgs1
Phenotype
vision/eye phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); homeostasis/metabolism phenotype;

Gene ontology

Biological process
phosphatidylglycerol biosynthetic process;cardiolipin biosynthetic process;diacylglycerol metabolic process
Cellular component
mitochondrion;mitochondrial inner membrane;endoplasmic reticulum
Molecular function
calcium ion binding;ATP binding;CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase activity